A genetic and spatial Bayesian analysis of mastitis resistance

A nationwide health card recording system for dairy cattle was introduced in Norway in 1975 (the Norwegian Cattle Health Services). The data base holds information on mastitis occurrences on an individual cow basis. A reduction in mastitis frequency across the population is desired, and for this purpose risk factors are investigated. In this paper a Bayesian proportional hazards model is used for modelling the time to first veterinary treatment of clinical mastitis, including both genetic and environmental covariates. Sire effects were modelled as shared random components, and veterinary district was included as an environmental effect with prior spatial smoothing. A non-informative smoothing prior was assumed for the baseline hazard, and Markov chain Monte Carlo methods (MCMC) were used for inference. We propose a new measure of quality for sires, in terms of their posterior probability of being among the, say 10% best sires. The probability is an easily interpretable measure that can be directly used to rank sires. Estimating these complex probabilities is straightforward in an MCMC setting. The results indicate considerable differences between sires with regards to their daughters disease resistance. A regional effect was also discovered with the lowest risk of disease in the south-eastern parts of Norway.     

Carex, subgenus Carex (Cyperaceae) – A phylogenetic approach using ITS sequences

To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed.     

A novel approach for assessing factors affecting biodiversity based on networks analysis

We propose in this work a novel approach aiming at assessing cause and effect relationships between variables that can affect target biodiversity issues. These cause–effect relations are used to build a network whose nodes represent variables linked by directed arcs. The arcs have associated a value that represents trends of cause–effect relations. An important novelty of this approach is the use of product and addition operations between trends of cause–effect relations for assessing factors that can affect target variables. For the analysis of the network we use the concept of paths. Paths are defined as sequences of cause–effect relations from source variables to target variables. For example, the path from population increment that causes effects on the increment of transport routes, which in turn causes effects on the loss of vegetation cover. This approach was applied to the assessment of vegetation cover in the Morelos State, México during the period 2000–2010. The results show a promising practical alternative to assess the potential effects on biodiversity issues based on the analysis of the paths represented in the network.     

Uncertainty and sensitivity analysis of West Java Water Sustainability Index – A case study on Citarum catchment in Indonesia

Water sustainability indices have been recently used to measure the sustainability of water resources within a catchment. Developing a sustainability index involves various steps, some of which have uncertainties associated with them. For the recently developed West Java Water Sustainability Index (WJWSI), three sources of uncertainties were identified, namely uncertainties in the thresholds of non-categorical indicators and sub-indicators, in the weighting schemes, and in the aggregation methods. This paper presents the uncertainty and sensitivity analysis of WJWSI, based on the application of WJWSI to Citarum catchment in West Java, Indonesia. The results of the uncertainty analysis, measured by the coefficient of variation of the thresholds and the sub-indices, indicates that minimum thresholds of Land Use Changes, Coverage, Education, Poverty, Health Impact and Sanitation, and the maximum threshold of Water Quality have higher variation when compared to variation of the other thresholds. The results of the sensitivity analysis, measured by the correlation coefficients between the final index and the thresholds, indicate that changes in the thresholds of WJWSI indicators have not significantly affected the sub-index values of most indicators and sub-indicators. The sensitivity analysis also concluded that either the equal or non-equal weighting scheme can be used for future use of the aggregation of WJWSI indicators and sub-indicators, as changes from equal to non-equal weighting scheme did not significantly affect the final index. However, it was found that the final index values were most sensitive to the aggregation method used (i.e. arithmetic and geometric methods), shown by the significant changes in the final index value when the aggregation method was changed from arithmetic to geometric. The uncertainty and sensitivity analysis presented in this study will not just assist in the efficient use of the WJWSI, but will also help undertake similar analysis for other indices.     

Normal human adipose tissue functions and differentiation in patients with biallelic LPIN1 inactivating mutations

Lipin-1 is a Mg²⁺-dependent phosphatidic acid phosphatase (PAP) that in mice is necessary for normal glycerolipid biosynthesis, controlling adipocyte metabolism, and adipogenic differentiation. Mice carrying inactivating mutations in the Lpin1 gene display the characteristic features of human familial lipodystrophy. Very little is known about the roles of lipin-1 in human adipocyte physiology. Apparently, fat distribution and weight is normal in humans carrying LPIN1 inactivating mutations, but a detailed analysis of adipose tissue appearance and functions in these patients has not been available so far. In this study, we performed a systematic histopathological, biochemical, and gene expression analysis of adipose tissue biopsies from human patients harboring LPIN1 biallelic inactivating mutations and affected by recurrent episodes of severe rhabdomyolysis. We also explored the adipogenic differentiation potential of human mesenchymal cell populations derived from lipin-1 defective patients. White adipose tissue from human LPIN1 mutant patients displayed a dramatic decrease in lipin-1 protein levels and PAP activity, with a concomitant moderate reduction of adipocyte size. Nevertheless, the adipose tissue develops without obvious histological signs of lipodystrophy and with normal qualitative composition of storage lipids. The increased expression of key adipogenic determinants such as SREBP1, PPARG, and PGC1A shows that specific compensatory phenomena can be activated in vivo in human adipocytes with deficiency of functional lipin-1.     

Eight microsatellite markers for the neotropical tree Luehea seemannii (Tiliaceae)

We isolated eight polymorphic microsatellites from the neotropical tree Luehea seemannii for gene flow and genetic structure studies. We used a streptavidin subtractive enrichment technique to develop a library of CA/GT repeats. Eight loci were screened for diversity from 96 individuals from Barro Colorado Island (BCI) and neighbouring Gigante peninsula in Panama. Luehea seemannii shows moderate levels of genetic diversity within these two populations. Allelic richness ranged from four to nine alleles and averaged 6.44 alleles per locus. Average expected heterozygosity was 0.65 on BCI and 0.60 on Gigante. Results are compared to microsatellite data from another wind‐dispersed gap colonizing species common in Panama.     

Spectrographic analysis of laryngeal air sac resonance in rhesus monkey.

Laryngeal air sacs are circular out-pocketings, located in the hyoid bone with their ostium in the midline of the anterior part of the larynx. From previous cadaver studies of the rhesus monkey it was deduced that the function of the air sac is to act as a resonating chamber. The present study was designed to test this hypothesis. Recordings were made of three rhesus monkeys before and after surgical removal of the air sac. Spectrographic analysis of the monkeys' vocalizations indicated that differences in formant frequency characteristics between pre-and post-surgical recordings were negligible. This finding suggests that the laryngeal air sac does not play an important role in the resonant properties of the monkeys' vocal tracts.     

Family resemblance for anthropometric and blood pressure measurements in Black Caribs and Creoles from St. Vincent Island

This paper examines family resemblance for five anthropometric measurements (height, weight, triceps skinfold, upper arm circumference relaxed [UACR] and flexed [UACF] and for systolic and diastolic blood pressure in a group of adult Caribbean islanders of primarily African ancestry. Six hypotheses about family resemblance are tested by using path analysis and likelihood ratios. Significant intergenerational transmission is found only for height and UACR. For weight, UACF, and diastolic blood pressure, non-transmissible sibling resemblance is the primary component of family resemblance, although significant marital resemblance exists for diastolic blood pressure. Triceps skinfold and systolic blood pressure show no evidence of any family resemblance. Although results for highly heritable traits such as height are comparable to reports from other populations, measurements with a large contribution from common family environment or residual environmental effects, such as triceps skinfold or blood pressure, have much lower family resemblance in this population than in other populations. We hypothesize that this difference is due to the fact that adult children and their parents do not share a common household in this culture and to the presence of major nonfamilial environmental factors contributing to obesity and hypertension in this population.     

Joint multiple quantitative trait loci mapping for allometries of body compositions and metabolic traits to body weights in broiler

In order to map quantitative trait loci (QTLs) for allometries of body compositions and metabolic traits in chicken, we phenotypically characterize the allometric growths of multiple body components and metabolic traits relative to BWs using joint allometric scaling models and then establish random regression models (RRMs) to fit genetic effects of markers and minor polygenes derived from the pedigree on the allometric scalings. Prior to statistically inferring the QTLs for the allometric scalings by solving the RRMs, the LASSO technique is adopted to rapidly shrink most of marker genetic effects to zero. Computer simulation analysis confirms the reliability and adaptability of the so-called LASSO-RRM mapping method. In the F₂ population constructed by multiple families, we formulate two joint allometric scaling models of body compositions and metabolic traits, in which six of nine body compositions are tested as significant, while six of eight metabolic traits are as significant. For body compositions, a total of 14 QTLs, of which 9 dominant, were detected to be associated with the allometric scalings of drumstick, fat, heart, shank, liver and spleen to BWs; while for metabolic traits, a total of 19 QTLs also including 9 dominant be responsible for the allometries of T4, IGFI, IGFII, GLC, INS, IGR to BWs. The detectable QTLs or highly linked markers can be used to regulate relative growths of the body components and metabolic traits to BWs in marker-assisted breeding of chickens.